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University of Strathclyde
University of Strathclyde
2024-10-22
Figure 1: Small molecules identified in previous HTS increase GCase activity.
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Issue
Dynamite plot: the lower extent of these error bars is not visible.
Solution
Use boxplots or 1D scatterplots
Issue
Incomplete presentation of statistical comparisons, e.g is there a difference between A16 and A18 in (B)?
Solution
Present a table of statistical differences instead, or alongside the figure.
Issue
Distance between bars makes comparison awkward.
Solution
Place things to be compared by the reader next to each other where possible, to facilitate visual comparison.
Issue
The scale on the micrographs (especially in panel C) is too small to read easily.
Solution
Increase the size of the scale relative to the figure so it can be read.
Issue
A visual control (bright-field image) is absent.
Solution
In addition to showing DAPI and immunofluorescence images of the cells, include a bright-field micrograph of the cells (no fluorescence).
Issue
The colour scheme is misleading because saturation represents different data across figure panels (compare 1 \(\mu\)M A18 in B vs 5 \(\mu\)M in D, and 1 \(\mu\)M A18 in E).
Solution
Be consistent with the visual messaging of colour (hue, saturation, and luminance).
Issue
Too many comparisons in B clutter the figure and compress the space available for showing data.
Solution
Present a table of statistical differences instead, or alongside the figure, to reduce clutter.
Issue
\(y\)-axis scales vary between panels, so quantitative comparison between panels is difficult.
Solution
Use the same \(y\)-axis scale in all panels to facilitate direct comparison.
Figure 2: Endometriosis-associated macrophages exhibit significant transcriptomic heterogeneity.
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| Suggestions for improvement |
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Issue
UMAP plots (B, E) are highly manipulable and clustering/placement does not necessarily reflect objective measures.
Solution
Be cautious of over-interpretation of UMAP and other nonlinear dimensionality reduction plots.
Issue
Unpleasant clashing (R default) colour choices in (C).
Solution
Use an appropriate colour palette.
Issue
The proportion plot in (C) does not give information on absolute number, only proportion/composition.
Solution
A proportional areas plot spanning all clusters would represent both absolute count per group and compositional information.
Issue
Heatmap text is too small to read comfortably.
Solution
Present heatmap as a separate figure, or reduce the amount of information in the image.
Issue
Heatmap is missing a scale (is purple high and yellow low, or vice versa?)
Solution
Add a scale bar.
Issue
The experimental summary in (A) does not indicate order of operations.
Solution
Use arrows to indicate order of steps and/or dataflow.
Issue
Text is too small in general to read comfortably.
Solution
Increase font size and/or break up the panels into individual figures.
Issue
The figure is crowded and the separation of panels is unclear.
Solution
Use whitespace to guide reader “flow” through the figure and reduce crowding -in particular, cramming (C) under the inset from (B) makes the figure feel very crowded. Alternatively break the panels into multiple figures.
Issue
The overall message of the figure is unclear.
Solution
If the intent is just that the macrophages exhibit transcriptional heterogeneity, then (D) is probably sufficient. If other messages are intended, then revise for clarity.
Figure 3: A C. difficile mutant lacking all three YkuD-type Ldts (\(\Delta\)ldt1-3) exhibits wild-type growth, morphology, and 3-3 cross-linking.
| Reasons for the grade |
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| Suggestions for improvement |
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Issue
Dynamite plot: the lower extent of these error bars is not visible.
Solution
Use boxplots or 1D scatterplots
Issue
No complement of the triple mutant strain - missing data for an essential control?
Solution
Ensure that all controls are presented so that the experimental result can be interpreted properly.
Issue
Label obscures part of the image.
Solution
Relocate the label so data is not obscured.
Issue
Fluorescence wavelength not specified.
Solution
Include sufficient information that the reader does not need to refer to the main text. Overall a figure legend should provide enough detail for the figure to stand alone, but should not describe results/significance.
Issue
Colour schemes/palettes are inconsistent within panel A, and between panels B, D, and E.
Solution
Be consistent with the visual messaging of colour (hue, saturation, and luminance).
Issue
Excessive length of figure legend for panel A.
Solution
Break out panel A into its own figure.
Figure 4: Functional characterization and overall structure of Rv1217c–1218c.
| Reasons for the grade |
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| Suggestions for improvement |
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Issue
The rifampicin structure is purely decorative.
Solution
Remove unnecessary elements and avoid needless distractions in figures.
Issue
Dynamite plot: the lower extent of these error bars is not visible.
Solution
Use boxplots or 1D scatterplots
Issue
Colour scheme in (B) doesn’t seem purposeful and doesn’t add anything to the figure.
Solution
Use colour consistently to link or distinguish elements/groups/data, rather than for decoration.
Issue
The meaning of the grey regions in (C) and (D) is unclear.
Solution
The implied membrane in (C) and (D) could be labelled as such in the figure. By convention in microbiology, we would assume that the periplasm/extracellular space is “up” and the cytoplasm is “down” in (C) and (D) - but this should really be labelled to avoid any potential confusion.
Issue
Colours in (A) difficult to distinguish, especially with the red boxes which seem to skew blue closer to purple.
Solution
Instead of well images, a heatmap with clearer colour distinction could be presented.
Issue
Showing two cut-out bands is not an appropriate way to show Western blot data.
Solution
Present the complete blot.
Issue
Text in (D) is too small to read easily.
Solution
Break out panel into a separate figure or increase font size.
BM432 Data Visualisation Workshop